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Scientist - Neural Data Analysis

Department: Systems Neuroscience

Scientist -  Neural Data Analysis – Systems Neuroscience


The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact on science.

The MindScope program seeks to understand the transformations, sometimes called computations, in coding and decoding that lead from photons to behavior and conscious experience by observing, perturbing, and modeling the physical transformations of signals in the cortical-thalamic visual system within a few perception-action cycles.

We are seeking a Scientist to be an essential team member in our ongoing efforts to link transcriptomically defined cell types with the types of functional neural activity in vivo. We are generating systematic datasets of neural activity using 2-photon calcium imaging in the mouse cortex, followed up by spatial transcriptomics, in order to better understand cell-type-specific contributions to neural coding and circuit dynamics.

The core responsibility for this position will be the computational analysis of these datasets, including co-registration between the calcium imaging and spatial transcriptomics data, linking these modalities for individual cells. The ideal candidate will have experience with analysis of imaging data, sensory physiology, machine learning, computer vision, and/or spatial transcriptomics. This position sits at the interface of neuroscience and data science, and good coding and analytical skills are a high priority.

The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences, and backgrounds. High-quality science can only be produced when it includes different perspectives. We are committed to increasing diversity across every team and encourage people from all backgrounds to apply for this role.

Essential Functions

  • In close collaboration with experimentalists and other analysts, work as a team member to analyze large-scale neurophysiological activity
  • Develop and apply the tools for linking neural activity of individual cells to their spatial transcriptomics characterization and, thus, their cell type
  • Contribute scientific ideas based on the analysis results
  • Publish/present findings in peer-reviewed journals and at scientific conferences
  • Maintain clear and accurate communication with supervisor and other team members

Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects management’s assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.

Required Education and Experience

  • PhD in Neuroscience, Computational Neuroscience, Computer Science, Applied Math or related field; or equivalent combination of degree and experience
  • Strong computational/data analysis skills; ideally programming in Python
  •     Track record of scientific excellence and independent thinking

Preferred Education and Experience

  • 0 – 7 years of relevant post-doctoral experience
  • Experience in systems neuroscience (especially in vivo neural measurements and/or sensory neuroscience)
  • Experience in bridging neurophysiology with spatial transcriptomics

Work Environment

  • May enter laboratory environment, including potential exposure to lasers, biohazards

Physical Demands

  • Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab equipment

Position Type / Expected Hours of Work

  • This role is currently able to work remotely due to COVID-19 and our focus on employee safety. We are a Washington State employer, and remote work must be performed in Washington State. We continue to evaluate the safest options for our employees. As restrictions are lifted in relation to COVID-19, this role will return to work onsite

Additional Eligibility Qualifications

  • In keeping with our focus on employee safety, all employees must be up to date with vaccinations against COVID-19 as a condition of employment unless a medical or religious accommodation is approved. All employees will be required to keep their vaccination status up to date according to CDC guidance.

Additional Comments

  • **Please note; This opportunity may offer relocation assistance**
  • **Please note; This opportunity may offer work visa sponsorship**


It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities.





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